A5000274356- Evolution and Genetic Dynamics
- Genetic diversity and population structure
- Genetic Mapping and Diversity in Plants and Animals
- Genetic Associations and Epidemiology
- Genomics and Phylogenetic Studies
- Genetic and phenotypic traits in livestock
- Forensic and Genetic Research
- Nitrogen and Sulfur Effects on Brassica
- Pleistocene-Era Hominins and Archaeology
- Forensic Anthropology and Bioarchaeology Studies
- Genetics, Bioinformatics, and Biomedical Research
- Evolutionary Algorithms and Applications
- Wheat and Barley Genetics and Pathology
- Chromosomal and Genetic Variations
- Gene Regulatory Network Analysis
- CRISPR and Genetic Engineering
- Berry genetics and cultivation research
- Bioinformatics and Genomic Networks
- Race, Genetics, and Society
- Epigenetics and DNA Methylation
- Plant Disease Resistance and Genetics
- Lipid metabolism and biosynthesis
- Milk Quality and Mastitis in Dairy Cows
- Yeasts and Rust Fungi Studies
- RNA and protein synthesis mechanisms
University of Wisconsin–Madison
2021-2025
Center for Research and Advanced Studies of the National Polytechnic Institute
2021-2023
Instituto Politécnico Nacional
2023
McGill University
2018-2021
McGill Genome Centre
2020-2021
Centre For Human Genetics
2018-2020
McGill University and Génome Québec Innovation Centre
2019-2020
University of Arizona
2015-2017
Applied Mathematics (United States)
2015-2017
Iowa State University
1946
Abstract Stochastic simulation is a key tool in population genetics, since the models involved are often analytically intractable and usually only way of obtaining ground-truth data to evaluate inferences. Because this, large number specialized programs have been developed, each filling particular niche, but with largely overlapping functionality substantial duplication effort. Here, we introduce msprime version 1.0, which efficiently implements ancestry mutation simulations based on...
Understanding variation in allele frequencies across populations is a central goal of population genetics. Classical models for the distribution frequencies, using forward simulation, coalescent theory, or diffusion approximation, have been applied extensively demographic inference, medical study design, and evolutionary studies. Here we propose tractable model ordinary differential equations evolution that closely related to approximation but avoids many its limitations approximations. We...
The explosion in population genomic data demands ever more complex modes of analysis, and increasingly, these analyses depend on sophisticated simulations. Recent advances genetic simulation have made it possible to simulate large models, but specifying such models for a particular engine remains difficult error-prone task. Computational genetics researchers currently re-implement independently, leading inconsistency duplication effort. This situation presents major barrier empirical seeking...
Despite broad agreement that Homo sapiens originated in Africa, considerable uncertainty surrounds specific models of divergence and migration across the continent
Latin America continues to be severely underrepresented in genomics research, and fine-scale genetic histories complex trait architectures remain hidden owing insufficient data1. To fill this gap, the Mexican Biobank project genotyped 6,057 individuals from 898 rural urban localities across all 32 states Mexico at a resolution of 1.8 million genome-wide markers with linked disease information creating valuable nationwide genotype-phenotype database. Here, using ancestry deconvolution...
We learn about population history and underlying evolutionary biology through patterns of genetic polymorphism. Many approaches to reconstruct histories focus on a limited number informative statistics describing distributions allele frequencies or linkage disequilibrium. show that many commonly used are part broad family two-locus moments whose expectation can be computed jointly rapidly under wide range scenarios, including complex multi-population demographies with continuous migration...
Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic datasets remains major obstacle. Today, more realistic are possible thanks to large increases quantity quality available genetic data, sophistication inference simulation software. However, implementing these still requires substantial time specialized knowledge. These challenges especially pronounced simulating genomes...
Abstract Demographic modelling is often used with population genomic data to infer the relationships and ages among populations. However, relatively few analyses are able validate these inferences independent data. Here, we leverage written records that describe distinct Brassica rapa crops corroborate demographic models of domestication. renowned for their outstanding morphological diversity, but order domestication remain unclear. We generated genomewide SNP s from 126 accessions collected...
Coalescent simulations are widely used to examine the effects of evolution and demographic history on genetic makeup populations. Thanks recent progress in algorithms data structures, simulators such as widely-used msprime now provide genome-wide for millions individuals. However, this software relies classic coalescent theory its assumptions that sample sizes small region being simulated is short. Here we show long regions genome exhibit large biases identity-by-descent (IBD), long-range...
As populations boom and bust, the accumulation of genetic diversity is modulated, encoding histories living in present-day variation. Many methods exist to decode these histories, all must make strong model assumptions. It typical assume that mutations accumulate uniformly across genome at a constant rate does not vary between closely related populations. However, recent work shows mutational processes human great ape genomic regions evolve over time. This perturbs mutation spectrum...
The study of domestication contributes to our knowledge evolution and crop genetic resources. Human selection has shaped wild Brassica rapa into diverse turnip, leafy, oilseed crops. Despite its worldwide economic importance potential as a model for understanding diversification under domestication, insights the number events initial crop(s) domesticated in B. have been limited due lack clarity about or feral status conspecific noncrop relatives. To address this gap reconstruct history rapa,...
Abstract Understanding the demographic history of populations is a key goal in population genetics, and with improving methods data, ever more complex models are being proposed tested. Demographic current interest typically consist set discrete populations, their sizes growth rates, continuous pulse migrations between those over number epochs, which can require dozens parameters to fully describe. There currently no standard format define such models, significantly hampering progress field....
The effect of a mutation on fitness may differ between populations depending environmental and genetic context, but little is known about the factors that underlie such differences. To quantify genome-wide correlations in effects, we developed novel concept called joint distribution effects (DFE) populations. We then proposed new statistic w to measure DFE correlation Using simulation, showed inferring from allele frequency spectrum statistically precise robust. population genomic data,...
Abstract Twentieth century industrial whaling pushed several species to the brink of extinction, with fin whales being most impacted. However, a small, resident population in Gulf California was not targeted by whaling. Here, we analyzed 50 whole-genomes from Eastern North Pacific (ENP) and (GOC) whale populations investigate their demographic history genomic effects natural human-induced bottlenecks. We show that two diverged ~16,000 years ago, after which ENP expanded then suffered 99%...
Abstract The magnitude of negative selection varies across the genome, affecting local levels diversity by virtue linked selection. Predicting patterns under such background has received considerable attention, and recent applications were able to explain a large portion variation in human genome. However, current models have yielded conflicting results, stemming from two key limitations. First, they display inaccuracies most critical region parameter space ( N e s ∼ −1), where reduction is...
Selection is a fundamental evolutionary force that shapes patterns of genetic variation across species. However, simulations incorporating realistic selection along heterogeneous genomes in complex demographic histories are challenging, limiting our ability to benchmark statistical methods aimed at detecting and explore theoretical predictions. stdpopsim community-maintained simulation library already provides an extensive catalog species-specific population models. Here we present major...
Many phenotypic traits are under stabilizing selection, which maintains a population’s mean value near some optimum. The dynamics of and trait architectures selection have been extensively studied for single populations at steady state. However, natural seldom state often structured in way. Admixture introgression events may be common, including over human evolutionary history. Because results against the minor allele trait-affecting locus, alleles from parental ancestry will selected after...
Simulation plays a central role in population genomics studies. Recent years have seen rapid improvements software efficiency that make it possible to simulate large genomic regions for many individuals sampled from numbers of populations. As the complexity demographic models we study grows, however, there is an ever-increasing opportunity introduce bugs their implementation. Here, describe two errors made defining genetic using msprime coalescent simulator found way into published record....
Population demographic history may be learned from contemporary genetic variation data. Methods based on aggregating the statistics of many single loci into an allele frequency spectrum (AFS) have proven powerful, but such methods ignore potentially informative patterns linkage disequilibrium (LD) between neighboring loci. To leverage patterns, we developed a composite-likelihood framework for inferring aggregated pairs Using this framework, show that two-locus are more sensitive to than...
Abstract Linkage disequilibrium (LD) is used to infer evolutionary history, identify genomic regions under selection, and dissect the relationship between genotype phenotype. In each case, we require accurate estimates of LD statistics from sequencing data. Unphased data present a challenge because multilocus haplotypes cannot be inferred exactly. Widely estimators for common r2 D2 exhibit large variable upward biases that complicate interpretation comparison across cohorts. Here, show how...
Selected mutations interfere and interact with evolutionary processes at nearby loci, distorting allele frequency trajectories creating correlations between pairs of mutations. Recent studies have used patterns linkage disequilibrium selected variants to test for selective interference epistatic interactions, some disagreement over interpreting observations from data. Interpretation is hindered by a lack analytic or even numerical expectations variation loci under the combined effects...
Abstract While it is now broadly accepted that Homo sapiens originated within Africa, considerable uncertainty surrounds specific models of divergence and migration across the continent. Progress hampered by a paucity fossil genomic data, as well variability in prior time estimates. Here we use linkage disequilibrium diversity-based statistics, optimized for rapid, complex demographic inference to discriminate among such models. We infer detailed populations including representatives from...
Abstract We learn about population history and underlying evolutionary biology through patterns of genetic polymorphism. Many approaches to reconstruct histories focus on a limited number informative statistics describing distributions allele frequencies or linkage disequilibrium. show that many commonly used are part broad family two-locus moments whose expectation can be computed jointly rapidly under wide range scenarios, including complex multi-population demographies with continuous...